This is a fun thread. I like where you and the grailkeeper are going with this. I think WAY more people should take much advantage of making up their own armies with their own story-lines. My chapter (the Galactic Watch) is vaguely based on Cromwell's New Model Army, for instance.
Frankly, I would not even worry about the Aquilas, Aquilia, Aquilettes... (what's the plural on that word?). Think how many nations in Europe alone used it? Byzantine Rome, the Seljuk Turks, the Holy Roman Empire, Austria, Spain, Albania, Tsarist Russia, Modern Russia, etc. These states were often at each other's throats under banners flying essentially the same symbol. The Galaxy is a lot bigger than Europe after all. There is plenty of room in the year 40,000 for multiple parties using the same symbol in my book. After all, who is to say that your chapter can't decide they are the "true" representatives of the spirit of the Aquila?